In that year, Kelby took over the position of chief engineer from Commander Charles Tucker, who had decided to take a transfer from Enterprise to the Columbia NX-02. Kelby soon found himself overwhelmed when Klingonsabotage threatened to destroy Enterprise, necessitating Tucker's return to the ship to purge a series of subroutines which prohibited Enterprise from dropping out of warp. Tucker subsequently decided to stay aboard temporarily to assist in making repairs, an act to which Kelby responded negatively, feeling that his position as chief engineer was in jeopardy. This tension came to a head when, under the influence of pheromones being produced by three Orion females who had boarded the ship, Kelby acted out his frustrations by disabling Enterprise and engaging in a fistfight with Tucker. (ENT: "Affliction", "Divergence", "Bound")

After Tucker returned full-time as Enterprise's chief engineer, Kelby remained on the engineering staff, and occasionally acted as acting-chief engineer in Tucker's absence, as he did later in 2155 when Tucker was kidnapped by the xenophobic terrorist group Terra Prime. In that capacity, Kelby oversaw the efforts to ensure that Enterprise could safely enter the tail of a comet headed for Mars to allow a shuttlepod to use the comet as camouflage to approach the planet undetected. Later, after the successful rescue of Tucker and Commander T'Pol, it was briefly believed that Kelby was responsible for an act of sabotage to the shuttlepod as his signature was on a shuttlepod maintenance log. It was soon determined that the saboteur could not have been Kelby as Tucker had transferred Kelby off of the responsible team upon his return from Columbia. Kelby's replacement, EnsignMasaro, was in fact, the Terra Prime sympathizer. (ENT: "Terra Prime")